LAMMPS docs (#80)

* added initial lammps docs.

* update to codeowners

Author: rubber-duck-debug

.github/CODEOWNERS

@@ -4,3 +4,4 @@ docs/software/communication @msimberg
 docs/software/devtools/linaro @jgphpc
 docs/software/prgenv/linalg.md @finkandreas @msimberg
 docs/software/sciapps/cp2k.md @abussy @RMeli
+docs/software/sciapps/lammps.md @nickjbrowning

docs/software/sciapps/lammps.md

@@ -1,4 +1,343 @@
 [](){#ref-uenv-lammps}
 # LAMMPS
-!!! todo
-    complete docs
+
+[LAMMPS](https://www.lammps.org/) is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. The current version of LAMMPS is written in C++.
+
+## Licensing Terms and Conditions
+
+[LAMMPS] is a freely-available open-source code, distributed under the terms of the [GNU Public License](http://www.gnu.org/copyleft/gpl.html).
+
+## Running  LAMMPS
+
+### Loading LAMMPS Interactively
+
+On Alps, [LAMMPS] is precompiled and available in a user environment (uenv). LAMMPS has been built with kokkos, and the GPU package separately.
+
+To find which LAMMPS uenv is provided, you can use the following command:
+
+```
+uenv image find lammps
+└── uenv image find lammps
+uenv/version:tag uarch date id size
+lammps/2024:v1      gh200  daint   3483b476b75a1801   3,713    2024-06-03
+lammps/2024:v2-rc1  gh200  daint   fc5aafe8f327553c   3,625    2025-02-05
+```
+
+We recommend using `lammps/2024:v2-rc1` as it's the latest build. To obtain this image, please run:
+
+```
+uenv image pull lammps/2024:v2-rc1
+```
+
+To start the uenv for this specific version of LAMMPS, you can use:
+
+```
+uenv start --view kokkos lammps/2024:v2-rc1
+```
+
+You can load the `view` from the uenv which contains the `lmp` executable. The executable in both these views support GPUs:
+
+```
+#lammps +kokkos packae
+uenv start --view kokkos lammps/2024:v2-rc1
+#lammps +gpu package, kokkos disabled
+uenv start --view gpu lammps/2024:v2-rc1
+```
+
+A development view is also provided, which contains all libraries and command-line tools necessary to build LAMMPS from source, without including the LAMMPS executable:
+
+```
+#build environment for lammps +kokkos package, without providing lmp executeable
+uenv start --view develop-kokkos lammps/2024:v2-rc1
+#build environment for lammps +gpu package, without providing lmp executeable
+uenv start --view develop-gpu lammps/2024:v2-rc1
+```
+
+### Running LAMMPS+kokkos on the HPC Platform
+
+To start  a job, two bash scripts are potentially required: a [slurm] submission script, and a wrapper for numacontrol which sets up cpu and memory binding:
+
+submission script:
+
+```bash title="run_lammps_kokkos.sh"
+#!/bin/bash -l
+#SBATCH --job-name=<JOB_NAME>
+#SBATCH --time=01:00:00
+#SBATCH --nodes=2                                                                        
+#SBATCH --ntasks-per-node=4
+#SBATCH --gres=gpu:4
+#SBATCH --account=<ACCOUNT>
+#SBATCH --uenv=<LAMMPS_UENV>:/user-environment
+#SBATCH --view=kokkos
+
+export MPICH_GPU_SUPPORT_ENABLED=1
+ 
+ulimit -s unlimited
+ 
+srun ./wrapper.sh lmp -in lj_kokkos.in -k on g 1 -sf kk -pk kokkos gpu/aware on
+```
+
+* Time format: `HH:MM:SS`.
+* For LAMMPS+kokkos its typical to only use 1 MPI-rank per GPU.
+* Change `<ACCOUNT>` to your project account name.
+* Change `<LAMMPS_UENV>` to the name (or path) of the LAMMPS uenv you want to use.
+
+numacontrol wrapper:
+
+```bash title="wrapper.sh"
+#!/bin/bash
+
+export LOCAL_RANK=$SLURM_LOCALID
+export GLOBAL_RANK=$SLURM_PROCID
+export GPUS=(0 1 2 3)
+export NUMA_NODE=$(echo "$LOCAL_RANK % 4" | bc)
+export CUDA_VISIBLE_DEVICES=${GPUS[$NUMA_NODE]}
+
+export MPICH_GPU_SUPPORT_ENABLED=1
+ 
+numactl --cpunodebind=$NUMA_NODE --membind=$NUMA_NODE "$@"
+```
+
+With the above scripts, you can launch a [LAMMPS] + kokkos calculation on 2 nodes, using 4 MPI-ranks per node and 4 GPUs per node with:
+
+```bash
+sbatch run_lammps_kokkos.sh
+```
+
+You may need to make the `wrapper.sh` script executeable via: `chmod +x wrapper.sh`.
+
+#### LAMMPS + kokkos input file
+
+Below is the input file used in the above script, defining a 3d Lennard-Jones melt.
+
+``` name="lj_kokkos.in"
+variable        x index 200
+variable        y index 200
+variable        z index 200
+variable        t index 1000
+
+variable        xx equal 1*$x
+variable        yy equal 1*$y
+variable        zz equal 1*$z
+
+variable        interval equal $t/2
+
+units           lj
+atom_style      atomic/kk
+
+lattice         fcc 0.8442
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
+mass            1 1.0
+
+velocity        all create 1.44 87287 loop geom
+
+pair_style      lj/cut/kk 2.5
+pair_coeff      1 1 1.0 1.0 2.5
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
+
+fix             1 all nve
+
+thermo          ${interval}
+thermo_style custom step time  temp press pe ke etotal density
+run_style       verlet/kk
+run             $t
+```
+
+### Running LAMMPS+GPU on the HPC Platform
+
+To start a job, 2 bash scripts are required:
+
+```bash title="run_lammps_gpu.sh"
+#!/bin/bash -l
+#SBATCH --job-name=<JOB_NAME>
+#SBATCH --time=01:00:00
+#SBATCH --nodes=2                                                                        
+#SBATCH --ntasks-per-node=32
+#SBATCH --gres=gpu:4
+#SBATCH --account=<ACCOUNT>                                                                  
+#SBATCH --uenv=<LAMMPS_UENV>:/user-environment
+#SBATCH --view=gpu
+
+export MPICH_GPU_SUPPORT_ENABLED=1
+ 
+ulimit -s unlimited
+
+srun ./mps-wrapper.sh lmp -sf gpu -pk gpu 4 -in lj.in
+```
+
+* Time format: `HH:MM:SS`.
+* For LAMMPS+gpu its often beneficial to use more than 1 MPI rank per GPU. To enable oversubscription of MPI ranks per GPU, you'll need to use the `mps-wrapper.sh` script provided at the following page: [NVIDIA GH200 GPU nodes: multiple ranks per GPU][ref-slurm-gh200-multi-rank-per-gpu]
+* Change `<ACCOUNT>` to your project account name.
+* Change `<LAMMPS_UENV>` to the name (or path) of the LAMMPS uenv you want to use.
+
+#### LAMMPS + kokkos input file
+
+Below is the input file used in the above script, defining a 3d Lennard-Jones melt.
+
+```
+# 3d Lennard-Jones melt
+variable        x index 200
+variable        y index 200
+variable        z index 200
+variable        t index 1000
+
+variable        xx equal 1*$x
+variable        yy equal 1*$y
+variable        zz equal 1*$z
+
+variable        interval equal $t/2
+
+units           lj
+atom_style      atomic
+
+lattice         fcc 0.8442
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
+mass            1 1.0
+
+velocity        all create 1.44 87287 loop geom
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0 2.5
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
+
+fix             1 all nve
+
+thermo          ${interval}
+thermo_style custom step time  temp press pe ke etotal density
+run_style       verlet
+run             $t
+```
+
+### Running on Eiger
+
+!!! TODO !!!
+
+### Building LAMMPS from source
+
+### Using CMake
+
+```
+If you'd like to rebuild LAMMPS from source to add additional packages or to use your own customized code, you can use the develop views contained within the uenv image to provide you with all the necessary libraries and command-line tools you'll need. For the following, we'd recommend obtaining an interactive node and building inside the tempfs directory.
+```
+
+```
+salloc -N1 -t 60 -A <account>
+...
+srun --pty bash
+...
+mkdir /dev/shm/lammps_build; cd /dev/shm/lammps_build
+```
+
+After you've obtained a version of LAMMPS you'd like to build, extract it in the above temporary folder, and create a build directory. Load one of the two following views:
+
+```
+#build environment for lammps +kokkos package, without providing lmp executeable
+uenv start --view develop-kokkos lammps/2024:v2-rc1
+#build environment for lammps +gpu package, without providing lmp executeable
+uenv start --view develop-gpu lammps/2024:v2-rc1
+```
+
+and now you can build your local copy of LAMMPS. For example to build with kokkos and the `MOLECULE` package enabled:
+
+```
+CC=mpicc CXX=mpic++ cmake \
+-DCMAKE_CXX_FLAGS=-DCUDA_PROXY \
+-DBUILD_MPI=yes\
+-DBUILD_OMP=no \
+-DPKG_MOLECULE=yes \
+-DPKG_KOKKOS=yes \
+-DEXTERNAL_KOKKOS=yes \
+-DKokkos_ARCH_NATIVE=yes \
+-DKokkos_ARCH_HOPPER90=yes \
+-DKokkos_ARCH_PASCAL60=no \
+-DKokkos_ENABLE_CUDA=yes \
+-DKokkos_ENABLE_OPENMP=yes \
+-DCUDPP_OPT=no \
+-DCUDA_MPS_SUPPORT=yes \
+-DCUDA_ENABLE_MULTIARCH=no \
+../cmake  
+```
+
+!!! `Warning` !!!
+
+If you are downloading LAMMPS from github or their website and intend to use kokkos for acceleration, there is an issue with cray-mpich and kokkos versions <= 4.3. For LAMMPS to work correctly on our system, you need a LAMMPS version which provides kokkos >= 4.4. Alternatively, the cmake variable `-DEXTERNAL_KOKKOS=yes` should force cmake to use the kokkos version (4.5.01) provided by the uenv, rather than the one contained within the lammps distribution.
+
+### Using LAMMPS uenv as an upstream Spack Instance
+
+If you'd like to extend the existing uenv with additional packages (or your own), you can use the provide LAMMPS uenv to provide all dependencies needed to build your customization. See https://eth-cscs.github.io/alps-uenv/uenv-compilation-spack/ for more information.
+
+First, set up an environment:
+
+```
+uenv start --view develop-gpu lammps/2024:v2-rc1
+
+git clone -b v0.23.0 https://github.com/spack/spack.git
+source spack/share/spack/setup-env.sh
+export SPACK_SYSTEM_CONFIG_PATH=/user-environment/config/
+```
+
+Then create the path and file `$SCRATCH/custom_env/spack.yaml`. We'll disable the KOKKOS package (and enable the GPU package via +cuda spec), and add the CG-SPICA package (via the +cg-spica spec) as an example. You can get the full list of options here: https://packages.spack.io/package.html?name=lammps.
+
+```
+spack:
+  specs:
+  - lammps@20240417 ~kokkos +cuda cuda_arch=90 +python +extra-dump +cuda_mps +cg-spica
+  packages:
+    all:
+      prefer:
+        - +cuda cuda_arch=90
+    mpi:
+      require: cray-mpich +cuda
+  view: true
+  concretizer:
+    unify: true
+```
+
+Then concretize and build (note, you will of course be using a different path):
+
+```
+spack -e $SCRATCH/custom_env/ concretize -f
+spack -e $SCRATCH/custom_env/ install
+```
+
+During concretization, you'll notice a hash being printed alongside the LAMMPS package name. Take note of this hash. If you now try to load LAMMPS:
+
+```
+# naively try to load  LAMMPS 
+# it shows two versions installed (the one in the uenv, and the one we just built)
+spack load lammps
+==> Error: lammps matches multiple packages.
+  Matching packages:
+    rd2koe3 [email protected]%[email protected] arch=linux-sles15-neoverse_v2
+    zoo2p63 [email protected]%[email protected] arch=linux-sles15-neoverse_v2
+  Use a more specific spec (e.g., prepend '/' to the hash).
+# use the hash thats listed in the output of the build
+# and load using the hash
+spack load /zoo2p63
+# check the lmp executable:
+which lmp
+/capstor/scratch/cscs/browning/SD-61924/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/lammps-20240417-zoo2p63rzyuleogzn4a2h6yj7u3vhyy2/bin/lmp
+```
+
+You should now see that the CG-SPICA package in the list of installed packages:
+
+```
+> lmp -h
+...
+Installed packages:
+
+CG-SPICA GPU KSPACE MANYBODY MOLECULE PYTHON RIGID
+```
+
+## Scaling
+
+!!! TODO !!!
+